Research workbench
Braf kinase domain B3AC loop deletion mutant in complex with dabrafenib
Analyse Braf kinase domain B3AC loop deletion mutant in complex with dabrafenib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HIE
- Type
- protein
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase B-RAF
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- P06
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 258 | 41% helix, 18% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 259 | 37% helix, 19% strand | P15056 |
| C, D | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 253 | 41% helix, 18% strand | P15056 |
Ligands and binding sites
- P06 · Dabrafenib · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.83 | 0.91 | 45 | P06 |
| 2 | 422 | 0.81 | 0.89 | 44 | P06 |
| 3 | 297 | 0.75 | 0.87 | 35 | P06 |
| 4 | 301 | 0.72 | 0.85 | 38 | P06 |
| 5 | 337 | 0.57 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–B · 774 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 749 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 749 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 448 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HIE · BRAF Kinase domain b3aC loop deletion mutant in complex with dabrafenib · the same entry in another collection · chain D against D, TM-score 1.00
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain C against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P15056
- Elsewhere: RCSB PDB 5HIE · PDBe 5HIE · UniProt P15056
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